Senior Scientist - De Novo Peptide Design [Remote]

We are seeking a Senior Scientist to design peptide ligands for delivery of RNA therapeutics. This role is an early hire on a growing delivery sciences team. The successful candidate makes major contributions to the ongoing development of the company's next generation blood-brain barrier-crossing delivery platform and will help shape future peptide work at Aerska, with growing responsibility and influence as the team scales.

Day to day, the successful candidate will carry out in silico de novo peptide design, set up and run the computational design pipeline, and generate peptide sequences for synthesis and evaluation by wet lab team members.

Key Responsibilities

Peptide Design & Computational Pipeline

• Set up and maintain the computational design pipeline, using generative AI tools such as RFpeptide and BoltzGen.
• Perform physics-based filtering of designs via molecular dynamics simulations (e.g. Amber, Schrödinger, or GROMACS) and docking (e.g. Rosetta FlexPepDock, HADDOCK, AutoDock CrankPep) to refine and prioritise candidates.
• Provide high-confidence peptide sequences for synthesis and wet lab validation.

Cross-Disciplinary Collaboration & Experimental Validation

• Interface with internal biophysical and peptide chemistry teams to coordinate peptide synthesis and wet lab testing.
• Translate experimental feedback into iterative improvements to peptide designs.
• Develop working knowledge of RNA therapeutics, oligonucleotide medicinal chemistry, and the principles of ligand-based delivery.
• Collaborate with wet lab colleagues to bring a computational perspective to shared problems.
• Act as a low-ego, self-starting contributor able to drive projects forward independently while staying closely aligned with the wider team.

Scientific Communication

• Keep clear documentation of designs and results.
• Present computational and experimental work internally and, when appropriate, externally.
• Educate leadership on emerging peptide design methods and advocate for their adoption.
• Communicate progress, results, and design rationale to wet lab peers and to leadership, keeping the design-build-test cycle moving.
• Work closely with the legal team to provide the information needed for intellectual property protection.

• PhD in Protein/Peptide Design, Computational Biology, Biophysics, Computational Chemistry, Peptide Chemistry, Bioinformatics or relevant field, with 2+ years of postdoc and/or industry experience.
• Demonstrable de novo peptide design experience.
• Hands-on experience building and running computational pipelines in Linux and cloud compute environments (AWS or similar).
• Track record of driving designs through to experimental validation.
• Proficiency with generative design tools (RFpeptide, BoltzGen, etc.).
• Peptide–protein docking experience (Rosetta FlexPepDock, HADDOCK, AutoDock CrankPep, etc.) is preferred.
• Familiarity with molecular dynamics simulations and analyses is preferred.
• Strong communication skills, with the confidence to advocate for your work and present effectively to leadership.
• Enthusiasm to learn the fundamentals of RNA therapeutics.
• Ability to effectively work with a cross-disciplinary team that includes chemistry, cell biology, and neuroscience.

Aerska is a values-driven organisation, guided by the belief that “we live in each other’s shelter”, reflecting our deep sense of interdependence and collaboration. Every member of the team is expected to embody our shared values:

• Walk on Air: Pursue bold ideas with ambition to solve meaningful problems that create real impact
• Time is Neurons: Every moment counts for patients – act with urgency and care, making data-driven decisions without compromise.
• Win or Learn: Embrace curiosity, adapt quickly and continuously improve
• We Before Me: Seek diverse perspectives, collaborate with humility, openness and respect, and prioritise collective success above individual advancement.